Turnover of the human proteome - determination of protein intracellular stability by dynamic SILAC

Mary K Doherty, Dean E Hammond, Michael J Clague, Simon J Gaskell, Robert J Beynon

Research output: Contribution to journalArticle

197 Citations (Scopus)

Abstract

The proteome of any system is a dynamic entity, such that the intracellular concentration of a protein is dictated by the relative rates of synthesis and degradation. In this work, we have analyzed time-dependent changes in the incorporation of a stable amino acid resolved precursor, a protocol we refer to as "dynamic SILAC", using 1-D gel separation followed by in-gel digestion and LC-MS/MS analyses to profile the intracellular stability of almost 600 proteins from human A549 adenocarcinoma cells, requiring multiple measures of the extent of labeling with stable isotope labeled amino acids in a classic label-chase experiment. As turnover rates are acquired, a profile can be built up that allows exploration of the 'dynamic proteome' and of putative features that predispose a protein to a high or a low rate of turnover. Moreover, measurement of the turnover rate of individual components of supramolecular complexes provides a unique insight in processes of protein complex assembly and turnover.
Original languageEnglish
Pages (from-to)104-12
Number of pages9
JournalJournal of Proteome Research
Volume8
Issue number1
DOIs
Publication statusPublished - Jan 2009

Keywords

  • Cell Line, Tumor
  • Databases, Protein
  • Electrophoresis, Polyacrylamide Gel
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Kinetics
  • Mass Spectrometry
  • Peptide Mapping
  • Protein Processing, Post-Translational
  • Proteins
  • Proteome
  • Proteomics
  • Ribosomes
  • Stochastic Processes
  • Time Factors

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